We began with an abstract computational problem: inference in a
Markov model. Following essentially Marr's
three-levels prescription [1]}, we characterized
the computational task (level 1), derived the necessary
representation and algorithm for solving it (level 2), and used these
to guide the design of a biochemical realization (level 3). In this process, however, we ended up with a biochemical circuit that does not map to the
abstract computation we had started out with in the
way one might naively expect. The logic of protein production—i.e., the synthesis/degradation of proteins and
the kinetics of these processes—constrained and shaped the computational task we
had started with.
